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Phylogenetic Analysis and Intrageneric Structure of the Genus Hyphornicrobium and the Related Genus Filornicrobium

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International Journal of Systematic Bacteriology (1 998), 48,635-639 Printed in Great Britain Phylogenetic analysis and intrageneric structure of the genus Hyphornicrobium and the related genus Filornicrobium Frederick A. Rainey,' Naomi Ward-Rainey,' Christian G. Gliesche2 and Erko Stackebrandtl Author for correspondence: Erko Stackebrandt. Tel: +49 531 26 16 352. Fax: +49 532 26 16 418. e-mail : erkoagbf-de Deutsche Sammlung von Almost complete 16s rDNA sequences from the type strains of seven species of Mikroorganismen und the genus Hyphomicrobium and of Filomicrobium fusiforme have been Zellkulturen GmbH, D- 381 24 Braunschweig, determined. The Hyphomicrobium species form two phylogenetic clusters that Germany are only moderately related to each other. While cluster I contains the type Inst it ut fur Al lgemei ne species Hyphomicrobium vulgare, Hyphomicrobium aestuarii, Hyphomicrobium Mikro biologie, U n iversitat hollandicum and Hyphomicrobium zavarzinii, cluster II comprises Kiel, Am Botanischen Hyphomicrobium facilis, Hyphomicrobium denitrificans and Hyphomicmbium Garten 1-9, 0-241 18 Kiel, Germany methylovomm. Within the two species clusters, the species are highly related. Phylogenetically,Filomicmbium fusiforme clusters moderately with Hyphomicrobium species. The lack of distinguishing phenotypical properties presently excludes the possibility of describing cluster II as a new genus. Keywords: Hyphomicrobium, Filomicrobium, intrageneric structure INTRODUCTION been isolated and included in these and in taxonomic studies (Gebers et al., 1986; Gliesche et al., 1988; Hyphomicrobia are appendaged bacteria that repro- Stackebrandt et al., 1988; Roggentin & Hirsch, 1989; duce by budding and have a dimorphic life cycle Holm et al., 1996). involving non-motile prosthecate mother cells and motile swarmer cells (Hirsch, 1989). In contrast to The genus Hyphomicrobium presently contains nine morphologically similar taxa such as Hyphomonas species (Hirsch, 1989; Urakami et al., 1995), one of (Moore & Weiner, 1989), Pedomicrobium (Gebers, which, H. coagulans (Takada, 1975), is not available 1989), Dichotomicrobium (Hirsch & Hoffmann, 1989), from any culture collection, while H. indicum has been Filomicrobium (Schlesner, 1987) or Rhodomicrobium discussed in the literature to be a non-authentic (Imhoff & Truper, 1989), hyphomicrobia are restricted member of the genus (Hirsch, 1989; Urakami et al., facultative methylotrophs capable of growth on 1995). Of the other species, only a few strains have reduced C, compounds such as methanol, methylated been included in chemotaxonomic studies (Guckert et amines or formate (Harder & Attwood, 1978). In al., 1991 ;Sittig & Hirsch, 1992) and in the phylogenetic recent years, hyphomicrobia became of special interest analysis of 16s rRNA (Stackebrandt et al., 1988; because of their versatility and ability to use toxic Roggentin & Hirsch, 1989; Tsuji et al., 1990) and 5s waste compounds that are not metabolized by other RNA sequences (Stackebrandt et al., 1988; Boulygina methylotrophs (Hanson, 1992). They can be used in et al., 1993). These studies have indicated that the the denitrification of sewage (Nyberg et al., 1992) or genus belongs to the alpha subclass of the class drinking water (Liessnes, 1993) or in the bio- Proteobacteria. However, according to the results of remediation of C, compounds such as halomethanes, DNA dot-blot hybridization studies on hundreds of methyl sulphates and methylated phosphates (Large & Hyphomicrobium strains (Holm et al., 1996), 19 DNA Bamforth, 1988) and, consequently, many strains have similarity clusters were identified, which points towards the presence of a significantly higher number of species than presently described. This paper is dedicated to Dr Peter Hirsch on the occasion of his 70th birthday. In this study, we present a phylogenetic analysis on all The EMBL accession numbers for the sequences reported in this paper are available type strains of the genus Hyphornicrobium, Y14302-Y14313. which will allow subsequent affiliation of environ- 00698 0 1998 IUMS 635 F. A. Rainey and others Table I. Bacterial strains analysed in this study ~~ Strain* Other designation(s)* Referencelsource H. aestuarii IFAM NQ-521grT ATCC 27488 Hirsch (1989) H. denitriJicansDSM 1869T TK 0415 = IFAM HA-905 Urakami et al. (1995) H. facilis subsp. facilis IFAM H-526T DSM 1565, ATCC 27485 Hirsch (1989) H. facilis IFAM B-522 Hirsch (1 989) H. facilis subsp. tolerans IFAM I-551T ATCC 27489 Hirsch (1 989) H.facilis subsp. ureaphilum IFAM CO-582T ATCC 27492 Hirsch (1989) H. hollandicum IFAM KB-677T ATCC 27498 Hirsch (1989) H. methylovorum DSM 5458T ATCC 35216, KM-146 Hirsch (1989) H. vulgare IFAM MC-750T ATCC 27500 Hirsch (1989) H. zavarzinii IFAM ZV-622T ATCC 27496 Hirsch (1989) H. zavarzinii IFAM ZV-580 Hirsch (1989) F. fusiforme DSM 5304T Schlesner (1987) * ATCC, American Type Culture Collection, Rockville, MD, USA; DSM, DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Germany ; IFAM, Institut fur Allgemeine Mikrobiologie, University of Kiel, Germany. mental isolates to known species and the recognition additional strains of Hyphomicrobium were sequenced. of novel genomic nuclei that may represent novel Their EMBL accession numbers are : Hyphomicrobium species. vulgare IFAM MC-750T (Y 14302), Hyphomicrobium hollandicum IFAM KB-677T (Y 14303), Hypho- METHODS microbium aestuarii IFAM NQ-52 lgrT (Y 14304), Hyphomicrobium zavarzinii IFAM ZV-622T (Y 14309, Bacterial strains. Strains analysed in this study are listed in Hyphomicrobium zavarzinii IFAM ZV-580 (Y 14306), Table 1. Growth media and culture conditions followed Hyphomicrobium methylovorum DSM 545gT(Y 14307), described procedures for the cultivation of Hyphomicrobium Hyphomicrobium denitrijicans DSM 1869T (Y 14308), strains (DSM catalogue of strains, 1993, 1996). Hyphomicrobium facilis subsp. facilis IFAM H-526T 165 rDNA sequence determination and analysis. Extraction (Y 14 309), Hyphom icr obium facil is subsp . ureaph ilum of genomic DNA, PCR-mediated amplification of the 16s IFAM CO-582T (Y 143lo), Hyphomicrobium facilis rDNA and sequence analysis of the purified PCR products subsp. tolerans IFAM I-551T (Y1431 l), Hypho- were performed as described previously (Rainey et al., 1996), microbium facilis IFAM B-522 (Y14312) and Filo- and the sequence reactions were electrophoresed using a microbium fusiforme DSM 5304T (Y 14313). model 373A automatic DNA sequencer (Applied Bio- systems). The length of sequences ranged between 1410 and 1446 To determine the closest relatives of strains of hypho- bases, which corresponded to 91 and 94% of the microbia, their phylogenetic position was determined Escherichia coli sequence (Brosius et al., 1978), re- initially using the database ARB (Strunk & Ludwig, 1995). A spectively. The position of the type strain of the type fine resolution of the relatedness between hyphomicrobia species of Hyphomicrobium was searched for in the and their closest relatives was perfomed using the ae2 editor ARB database (Strunk & Ludwig, 1995), and the (Maidak et al., 1994). Phylogenetic dendrograms were position within the ' Rhodomicrobium vannielii assem- reconstructed using treeing algorithms contained in the blage' (Maidak et al., 1994) could be confirmed. PHYLIP package (Felsenstein, 1993). Bootstrap values were determined using the PHYLIP package (Felsenstein, 1993). Subsequent phylogenetic analysis was carried out using the ae2 editor. The sequences of Hypho- Nucleotide sequence accession numbers. The accession microbium strains and of Filomicrobium fusiforme were numbers of the 16s rDNAs of references strains were: aligned with each other and with representatives of Agrobacterium tumefaciens, X67223 ; Methylobacterium organophilum, M29028 ; Methy lobacterium extorquens, neighbouring taxa. A total of 1360 nucleotides were M29027 ; Phyllobacteriurn myrsinacearum, D 12789; Meso- used in the analysis, and phylogenetic trees were rhizobium loti, D12791; Rhodobium rnarinum, D30790; generated using the algorithms of De Soete (1983) and Rhodobium orientis, D30792 ; and Rhodomicrobium vannielii, those included in the PHYLIP package (Felsenstein, M34127. 1993). All trees showed very similar topologies, in that all hyphomicrobia as well as F. fusiforme formed a phylogenetically coherent group, which was most RESULTS closely related to Rhodomicrobium vannielii (around The almost complete primary structure of the 16s 90% 16s rDNA sequence similarity), while the other rDNA of eight type strains of Hyphomicrobium species reference organisms were more distantly related (be- and of Filomicrobium fusiforme as well as of four tween 87 and 89.5 YOsimilarity). The only differences in 636 International Journal of Systematic Bacteriology 48 Phylogeny of Hyphomicrobium and Filomicrobium .................... ... .............................................................................. Rhodobium orientis Fig. 7- Dendrogram showing the Rhodobium marinum phylogenetic position of the genera Phyllobacterium myninacearum r-c+=FFMesorhizobium loti Hyphomicrobium and Filomicrobium among Agro bacterium turne fa ciens members of the alpha-2 subclass of the class Rhodomicrobium vannielii Proteobacteria. The tree was constructed by Hyphomicrobium facilis su bsp. ureaphilum CO-582T the neighbour-joining method (Saitou & Hyphomicrobium facilis subsp. tolerans I-551T Nei, 1987), using corrected distance values Hyphomicrobium facilis B-522 Hyphomicrobium facilis su bsp. facilis H-526T (Jukes & Cantor, 1969). The sequences
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    The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT.
  • Genetic and Phenetic Analyses of Bradyrhizobium Strains Nodulating Peanut (Arachis Hypogaea L.) Roots DIMAN VAN ROSSUM,1 FRANK P

    Genetic and Phenetic Analyses of Bradyrhizobium Strains Nodulating Peanut (Arachis Hypogaea L.) Roots DIMAN VAN ROSSUM,1 FRANK P

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 1995, p. 1599–1609 Vol. 61, No. 4 0099-2240/95/$04.0010 Copyright q 1995, American Society for Microbiology Genetic and Phenetic Analyses of Bradyrhizobium Strains Nodulating Peanut (Arachis hypogaea L.) Roots DIMAN VAN ROSSUM,1 FRANK P. SCHUURMANS,1 MONIQUE GILLIS,2 ARTHUR MUYOTCHA,3 1 1 1 HENK W. VAN VERSEVELD, ADRIAAN H. STOUTHAMER, AND FRED C. BOOGERD * Department of Microbiology, Institute for Molecular Biological Sciences, Vrije Universiteit, BioCentrum Amsterdam, 1081 HV Amsterdam, The Netherlands1; Laboratorium voor Microbiologie, Universiteit Gent, B-9000 Ghent, Belgium2; and Soil Productivity Research Laboratory, Marondera, Zimbabwe3 Received 15 August 1994/Accepted 10 January 1995 Seventeen Bradyrhizobium sp. strains and one Azorhizobium strain were compared on the basis of five genetic and phenetic features: (i) partial sequence analyses of the 16S rRNA gene (rDNA), (ii) randomly amplified DNA polymorphisms (RAPD) using three oligonucleotide primers, (iii) total cellular protein profiles, (iv) utilization of 21 aliphatic and 22 aromatic substrates, and (v) intrinsic resistances to seven antibiotics. Partial 16S rDNA analysis revealed the presence of only two rDNA homology (i.e., identity) groups among the 17 Bradyrhizobium strains. The partial 16S rDNA sequences of Bradyrhizobium sp. strains form a tight similarity (>95%) cluster with Rhodopseudomonas palustris, Nitrobacter species, Afipia species, and Blastobacter denitrifi- cans but were less similar to other members of the a-Proteobacteria, including other members of the Rhizobi- aceae family. Clustering the Bradyrhizobium sp. strains for their RAPD profiles, protein profiles, and substrate utilization data revealed more diversity than rDNA analysis. Intrinsic antibiotic resistance yielded strain- specific patterns that could not be clustered.